It doesn't look very elegant.

Checking the reference type twice is not elegant. More importantly, it doesn't work since you only handle HASH (and not ARRAY and non-refs) at the outer level.

_iterative_copy( [ 'a' ] );
[download]

outputs

What's a ARRAY at script.pl line 12
        main::_iterative_copy('ARRAY(0x15d5f18)') called at script.pl 
+line 47
[download]

Working code:

use strict;
use warnings;

use Data::Dumper qw( Dumper );

sub iterative_copy {
   my $root;
   my @src;
   my @dst;

   push @src, $_[0];
   push @dst, \$root;

   while (@src) {
      my $src = shift(@src);
      my $dst = shift(@dst);

      if (not ref $src) {
         $$dst = $src;
      }
      elsif (ref $src eq "HASH") {
         $dst = ($$dst = {});
         foreach my $key (keys %$src) {
            push @src, $src->{$key};
            push @dst, \($dst->{$key});
         }
      }
      elsif (ref $src eq "ARRAY") {
         $dst = ($$dst = []);
         foreach my $i (0..$#$src) {
            push @src, $src->[$i];
            push @dst, \($dst->[$i]);
         }
      }
      else {
         Carp::croak "What's a " . ref $_ . "?" 
      }
   }

   return $root;
}

{
   local $Data::Dumper::Indent = 0;

   my $d1 = [ [ 'a', 'b' ], { k1=>'v1', k2=>'v2' } ];
   my $d2 = iterative_copy($d1);

   print(Dumper($d1), "\n");
   print(Dumper($d2), "\n");

   print($d1,      " != ", $d2,      "\n");
   print($d1->[0], " != ", $d2->[0], "\n");
   print($d1->[1], " != ", $d2->[1], "\n");
}
[download]

Output:

$VAR1 = [['a','b'],{'k2' => 'v2','k1' => 'v1'}];
$VAR1 = [['a','b'],{'k2' => 'v2','k1' => 'v1'}];
ARRAY(0x1ae0718) != ARRAY(0x1ae073c)
ARRAY(0x15d5fd8) != ARRAY(0x1ae076c)
HASH(0x15d6c98) != HASH(0x1ae0790)
[download]

Below is a more elegant version. It uses one array (@todo) instead of two (@src, @dst). However, it uses more memory.